SMTL ID : 8pz6.1

crystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 analog 56

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x IG5: (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{S},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,6,7,8,9,9~{a}-octahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-(3-oxidanylpropylidene)cyclohexane-1,3-diol

IG5.1: 24 residues within 4Å: Chain A: T.23, Y.24, D.25, Y.28, F.31, L.107, L.110, V.111, Y.113, S.114, I.145, I.148, R.151, S.152, S.155, W.163, C.165, V.177, H.182, L.190, H.272, Y.276, L.279, F.297 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.28, A:F.31, A:L.107, A:L.107, A:L.107, A:L.110, A:V.111, A:I.145, A:I.148, A:W.163, A:V.177, A:V.177, A:L.190, A:Y.276, A:L.279, A:F.297 Hydrogen bonds: A:T.23, A:Y.24, A:D.25, A:R.151, A:R.151, A:R.151, A:S.155, A:H.272 IG5.2: 24 residues within 4Å: Chain C: T.23, Y.24, D.25, Y.28, F.31, L.107, L.110, V.111, Y.113, S.114, I.145, I.148, R.151, S.152, S.155, W.163, C.165, V.177, H.182, L.190, H.272, Y.276, L.279, F.297 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.28, C:F.31, C:L.107, C:L.107, C:L.107, C:L.110, C:V.111, C:I.145, C:I.148, C:W.163, C:V.177, C:V.177, C:L.190, C:Y.276, C:L.279, C:F.297 Hydrogen bonds: C:T.23, C:Y.24, C:Y.24, C:D.25, C:R.151, C:R.151, C:R.151, C:S.155, C:H.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fabisiak, A. et al., Design, synthesis, and biological activity of D-bishomo-1 alpha ,25-dihydroxyvitamin D 3 analogs and their crystal structures with the vitamin D nuclear receptor. Eur.J.Med.Chem. (2024)

Release Date

2024-04-24

Peptides

Vitamin D3 receptor A: AC
Nuclear receptor coactivator 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Vitamin D3 receptor A

Nuclear receptor coactivator 2

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